帳號:guest(18.218.221.126)          離開系統
字體大小: 字級放大   字級縮小   預設字形  

詳目顯示

以作者查詢圖書館館藏以作者查詢臺灣博碩士論文系統以作者查詢全國書目勘誤回報
作者:羅日彥
作者(英文):Jih-Yen Lo
論文名稱:In Silico Prediction of n-Octanol–Water Partition Coefficient by Various Data Fusion Methods
論文名稱(英文):In Silico Prediction of n-Octanol–Water Partition Coefficient by Various Data Fusion Methods
指導教授:梁剛荐
指導教授(英文):Max K. Leong
口試委員:翁慶豐
張秀華
口試委員(英文):Ching-Feng Weng
A. Hsiu-Hwa Chang
學位類別:碩士
校院名稱:國立東華大學
系所名稱:化學系
學號:610512015
出版年(民國):109
畢業學年度:108
語文別:英文
論文頁數:294
關鍵詞(英文):Partition coefficientdata fusionmachine learning
相關次數:
  • 推薦推薦:0
  • 點閱點閱:4
  • 評分評分:系統版面圖檔系統版面圖檔系統版面圖檔系統版面圖檔系統版面圖檔
  • 下載下載:3
  • 收藏收藏:0
Log P is an important physicochemical characteristic and it can express the lipophilicity of a compound. The lipophilic property is according to the biodistribution of drugs. In the drug discovery, log P is also an important filter characteristic to screen the candidate of medications. The experimental methods usually need more chemicals, and cost time. Building a model can fast and massive estimate the log P values. One approach of data fusion was applied to fuse the predictive packages by traditional schemes and machine learning schemes in this study. In addition, the data manipulation retrieve also adopted to increase performance of traditional schemes. In traditional schemes, arithmetic mean (SUM) based on consistent data had the best statistical assessments, the statistical assessments gave r2 (0.91), rm2 (0.90), s (0.51), RMSE (0.51), ΔMax (3.63), and MAE (0.36); in machine learning schemes, deep neural network (DNN) showed the best results, the statistical parameters presented r2 (0.98), rm2 (0.97), s (0.26), RMSE (0.27), ΔMax (1.88), and MAE (0.16). Overall, traditional schemes can fastly compute the data to enhance the data screening, and machine learning schemes provide the better log P prediction.
1. Introduction 1
2. Materials and Methods 5
2.1 Data Sources 5
2.2 Predictive Packages 5
2.3 Data Fusion by Traditional Schemes 6
2.3.1 Traditional Schemes Based on All Data 6
2.3.2 Traditional Schemes Based on Consistent Data 6
2.3.3 Traditional Schemes Based on Purged Data 6
2.4 Data Fusion by Support Vector Regression 6
2.5 Data Fusion by Extreme Learning Machine 7
2.6 Data Fusion by Deep Neural Network 7
2.7 Data Partition 8
2.8 Predictive Evaluation 8
3. Results 11
3.1 Data Partition 11
3.2 Traditional Schemes 11
3.3 Machine Learning Schemes 13
4. Discussion 15
5. Conclusion 17
6. References 19
Andrés, A., Rosés, M., Ràfols, C., Bosch, E., Espinosa, S., Segarra, V., & Huerta, J. M. (2015). Setup and validation of shake-flask procedures for the determination of partition coefficients (logD) from low drug amounts. Eur. J. Pharm. Sci., 76, 181-191. doi:10.1016/j.ejps.2015.05.008
Arnott, J. A., Kumar, R., & Planey, S. L. (2013). Lipophilicity Indices for Drug Development J. Appl. Biopharm. Pharmacokinet., 1, 31-36 doi:10.14205/2309-4435.2013.01.01.6
Atkinson, H. C., & Begg, E. J. (1988). Relationship between Human Milk Lipid-Ultrafiltrate and Octanol-Water Partition Coefficients. J. Pharm. Sci., 77(9), 796-798. doi:10.1002/jps.2600770916
Austin, R. P., Davis, A. M., & Manners, C. N. (1995). Partitioning of ionizing molecules between aqueous buffers and phospholipid vesicles. J. Pharm. Sci., 84(10), 1180-1183. doi:10.1002/jps.2600841008
Avery, M. A., Bonk, J. D., Chong, W. K. M., Mehrotra, S., Miller, R., Milhous, W., . . . Wyandt, C. (1995). Structure-Activity Relationships of the Antimalarial Agent Artemisinin. 2. Effect of Heteroatom Substitution at O-11: Synthesis and Bioassay of N-Alkyl-11-aza-9-desmethylartemisinins. J. Med. Chem., 38(26), 5038-5044. doi:10.1021/jm00026a011
Bajusz, D., Rácz, A., & Héberger, K. (2019). Comparison of Data Fusion Methods as Consensus Scores for Ensemble Docking. Molecules, 24(15), 2690. doi:10.3390/molecules24152690
Belkin, N. J., Kantor, P., Fox, E. A., & Shaw, J. A. (1995). Combining the evidence of multiple query representations for information retrieval. Inf. Process. Manage., 31(3), 431-448. doi:10.1016/0306-4573(94)00057-A
Cheng, T., Zhao, Y., Li, X., Lin, F., Xu, Y., Zhang, X., . . . Lai, L. (2007). Computation of Octanol−Water Partition Coefficients by Guiding an Additive Model with Knowledge. Journal of Chemical Information and Modeling, 47(6), 2140-2148. doi:10.1021/ci700257y
Chi, C.-T., Lee, M.-H., Weng, C.-F., & Leong, M. K. (2019). In Silico Prediction of PAMPA Effective Permeability Using a Two-QSAR Approach. Int. J. Mol. Sci., 20(13), 3170. doi:10.3390/ijms20133170
Chirico, N., & Gramatica, P. (2012). Real External Predictivity of QSAR Models. Part 2. New Intercomparable Thresholds for Different Validation Criteria and the Need for Scatter Plot Inspection. J. Chem. Inf. Model., 52(8), 2044-2058. doi:10.1021/ci300084j
Clark, D. E., & Pickett, S. D. (2000). Computational methods for the prediction of ‘drug-likeness’. Drug Discovery Today, 5(2), 49-58. doi:10.1016/S1359-6446(99)01451-8
Cortes, C., & Vapnik, V. (1995). Support-vector networks. Mach. Learn., 20(3), 273-297. doi:10.1007/BF00994018
Dearden, J. C., & Bresnen, G. M. (1988). The Measurement of Partition Coefficients. Quant. Struct.-Act. Relat., 7(3), 133-144. doi:10.1002/qsar.19880070304
Ding, Y.-L., Lyu, Y.-C., & Leong, M. K. (2017). In silico prediction of the mutagenicity of nitroaromatic compounds using a novel two-QSAR approach. Toxicol. In Vitro, 40, 102-114. doi:10.1016/j.tiv.2016.12.013
Ghose, A. K., & Crippen, G. M. (1986). Atomic Physicochemical Parameters for Three-Dimensional Structure-Directed Quantitative Structure-Activity Relationships I. Partition Coefficients as a Measure of Hydrophobicity. J. Comput. Chem., 7(4), 565. doi:10.1002/jcc.540070419
Ginn, C. M. R., Turner, D. B., Willett, P., Ferguson, A. M., & Heritage, T. W. (1997). Similarity Searching in Files of Three-Dimensional Chemical Structures:  Evaluation of the EVA Descriptor and Combination of Rankings Using Data Fusion. J. Chem. Inf. Comput. Sci., 37(1), 23-37. doi:10.1021/ci960466u
Golbraikh, A., Shen, M., Xiao, Z., Xiao, Y.-D., Lee, K.-H., & Tropsha, A. J. J. o. C.-A. M. D. (2003). Rational selection of training and test sets for the development of validated QSAR models. J. Comput.-Aided Mol. Des., 17(2), 241-253. doi:10.1023/a:1025386326946
Hall, D. L., & Llinas, J. (1997). An introduction to multisensor data fusion. Proc. IEEE, 85(1), 6-23. doi:10.1109/5.554205
Hansch, C., Leo, A., & Hoekman, D. (1995). Exploring QSAR: Hydrophobic, Electronic, and Steric Constants (Vol. 2). Washington, DC: American Chemical Society.
Harnisch, M., Möckel, H. J., & Schulze, G. (1983). Relationship between log Pow, shake-flask values and capacity factors derived from reversed-phase high-performance liquid chromatography for n-alkylbenzenes and some oecd reference substances. J. Chromatogr. A, 282, 315-332. doi:10.1016/S0021-9673(00)91610-8
Huang, G.-B., Zhu, Q.-Y., & Siew, C.-K. (2004, 25-29 July 2004). Extreme learning machine: a new learning scheme of feedforward neural networks. Paper presented at the 2004 IEEE International Joint Conference on Neural Networks (IEEE Cat. No.04CH37541).
Huang, G.-B., Zhu, Q.-Y., & Siew, C.-K. (2006). Extreme learning machine: Theory and applications. Neurocomputing, 70(1), 489-501. doi:10.1016/j.neucom.2005.12.126
Huang, G., Zhou, H., Ding, X., & Zhang, R. (2012). Extreme Learning Machine for Regression and Multiclass Classification. IEEE Trans. Syst. Man Cybern. Part B-Cybern., 42(2), 513-529. doi:10.1109/TSMCB.2011.2168604
Hubert, M., & Engelen, S. (2004). Robust PCA and classification in biosciences. Bioinformatics, 20(11), 1728-1736. doi:10.1093/bioinformatics/bth158 %J Bioinformatics
Kearsley, S. K., Sallamack, S., Fluder, E. M., Andose, J. D., Mosley, R. T., & Sheridan, R. P. (1996). Chemical Similarity Using Physiochemical Property Descriptors. J. Chem. Inf. Comput. Sci., 36(1), 118-127. doi:10.1021/ci950274j
Kril, M. B., & Fung, H.-L. (1990). Influence of hydrophobicity on the ion exchange selectivity coefficients for aromatic amines. J. Pharm. Sci., 79(5), 440-443. doi:10.1002/jps.2600790517
Lee, M.-H., Ta, G. H., Weng, C.-F., & Leong, M. K. (2020). In Silico Prediction of Intestinal Permeability by Hierarchical Support Vector Regression. Int. J. Mol. Sci., 21(10), 3582. doi:10.3390/ijms21103582
Leeson, P. D., & Springthorpe, B. (2007). The influence of drug-like concepts on decision-making in medicinal chemistry. Nat. Rev. Drug Discov., 6(11), 881-890. doi:10.1038/nrd2445
Leo, A., Hansch, C., & Elkins, D. (1971). Partition coefficients and their uses. Chem. Rev., 71(6), 525-616. doi:10.1021/cr60274a001
Leong, M. K., Chen, Y.-M., & Chen, T.-H. (2009). Prediction of human cytochrome P450 2B6-substrate interactions using hierarchical support vector regression approach. J. Comput. Chem., 30(12), 1899-1909. doi:10.1002/jcc.21190
Leong, M. K., Lin, S.-W., Chen, H.-B., & Tsai, F.-Y. (2010). Predicting Mutagenicity of Aromatic Amines by Various Machine Learning Approaches. Toxicol. Sci., 116(2), 498-513. doi:10.1093/toxsci/kfq159 %J Toxicological Sciences
Liao, Q., Yao, J., & Yuan, S. (2006). SVM approach for predicting LogP. Mol. Diversity, 10(3), 301-309. doi:10.1007/s11030-006-9036-2
Lipinski, C. A., Lombardo, F., Dominy, B. W., & Feeney, P. J. (1997). Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Advanced Drug Delivery Reviews, 23(1), 3-25. doi:10.1016/S0169-409X(96)00423-1
Meylan, W. M., & Howard, P. H. (2000). Estimating log P with atom/fragments and water solubility with log P. Perspect. Drug Discovery Des., 19(1), 67-84. doi:10.1023/A:1008715521862
Molnár, L., Keserű, G. M., Papp, Á., Gulyás, Z., & Darvas, F. (2004). A neural network based prediction of octanol–water partition coefficients using atomic5 fragmental descriptors. Bioorg. Med. Chem. Lett., 14(4), 851-853. doi:10.1016/j.bmcl.2003.12.024
Moriguchi, I., Hirono, S., Liu, Q., Nakagome, I., & Matsushita, Y. (1992). Simple Method of Calculating Octanol/Water Partition Coefficient. CHEM. PHARM. BULL., 40(1), 127-130. doi:10.1248/cpb.40.127
Ojha, P. K., Mitra, I., Das, R. N., & Roy, K. (2011). Further exploring rm2 metrics for validation of QSPR models. Chemometrics Intell. Lab. Syst., 107(1), 194-205. doi:10.1016/j.chemolab.2011.03.011
Ranadive, S. A., Chen, A. X., & Serajuddin, A. T. M. J. P. R. (1992). Relative Lipophilicities and Structural-Pharmacological Considerations of Various Angiotensin-Converting Enzyme (ACE) Inhibitors. Pharm. Res., 9(11), 1480-1486. doi:10.1023/a:1015823315983
Roy, K., Mitra, I., Kar, S., Ojha, P. K., Das, R. N., & Kabir, H. (2012). Comparative Studies on Some Metrics for External Validation of QSPR Models. J. Chem Inf. Model., 52(2), 396-408. doi:10.1021/ci200520g
Sangster, J. (1989). Octanol‐Water Partition Coefficients of Simple Organic Compounds. J. Phys. Chem. Ref. Data, 18(3), 1111-1229. doi:10.1063/1.555833
Schmidhuber, J. (2015). Deep learning in neural networks: An overview. Neural Netw., 61, 85-117. doi:10.1016/j.neunet.2014.09.003
Sheridan, R. P., Miller, M. D., Underwood, D. J., & Kearsley, S. K. (1996). Chemical Similarity Using Geometric Atom Pair Descriptors. J. Chem. Inf. Comput. Sci., 36(1), 128-136. doi:10.1021/ci950275b
Teijeiro, S. A., Moroni, G. N., Motura, M. I., & Briñón, M. C. (2000). Lipophilic character of pyrimidinic nucleoside derivatives: correlation between shake flask, chromatographic (RP-TLC and RP-HPLC) and theoretical methods. J. Liq. Chromatogr. Relat. Technol., 23(6), 855-872. doi:10.1081/JLC-100101494
Tropsha, A., Gramatica, P., & Gombar, V. K. (2003). The Importance of Being Earnest: Validation is the Absolute Essential for Successful Application and Interpretation of QSPR Models. QSAR Comb. Sci., 22(1), 69-77. doi:10.1002/qsar.200390007
Valkó, K. (2004). Application of high-performance liquid chromatography based measurements of lipophilicity to model biological distribution. Journal of Chromatography A, 1037(1), 299-310. doi:10.1016/j.chroma.2003.10.084
Willett, P. (2006). Enhancing the Effectiveness of Ligand-Based Virtual Screening Using Data Fusion. QSAR Comb. Sci., 25(12), 1143-1152. doi:10.1002/qsar.200610084
Willett, P. (2013). Combination of Similarity Rankings Using Data Fusion. J. Chem. Inf. Model., 53(1), 1-10. doi:10.1021/ci300547g

 
 
 
 
第一頁 上一頁 下一頁 最後一頁 top

相關論文

1. 利用Pharmacophore Ensemble/Support Vector Machine方法預測ABCG2抑制劑結合親和力
2. 使用Hierarchical Support Vector Regression發展Quantiative Structure Activity Relationship模型預測芳香族硝基化合物的致突變
3. 使用Support Vector Machine發展 SVM-Pose/SVM-Score Ensemble Docking 應用於預測N-methyl-D-aspartate的生物 活性
4. 利用Hierarchical Support Vector Machine方法預測血腦障蔽的穿透能力
5. 利用Pharmacophore Ensemble/Support Vector Machine方法預測Estrogen Receptor Alpha結合親和力
6. 利用不同的MachineLearning的方法去預測血腦障壁的穿透能力
7. 利用不同MachineLearningApproaches預測芳香族胺在沙門氏菌TA100中致癌/致突變的機率
8. 利用PharmacophoreEnsemble/SupportVectorMachineApproach預測人類多重藥物傳送蛋白P-Glycoprotein的抑制活性
9. 利用PharmacophoreEnsemble/SupportVectorMachine方法預測人類PregnaneXReceptor的活性化
10. 利用階層式支持向量回歸法預測人體多藥轉運醣蛋白介導的外排率
11. 使用Hierarchical Support Vector Regression方法預測血腦屏障的滲透表面積乘積
12. 利用階層式支持向量回歸法預測空腸的滲透率
13. 利用Hierarchical Support Vector Regression預測正辛醇 - 水分配係數
14. In Silico Prediction of Caco-2 Permeability by Quantitative Structure Activity Relationship Modeling Based on Hierarchical Support Vector Regression
15. 使用Pharmacophore Ensemble/Support Vector Machine (PhE/SVM)模型來預測Breast Cancer Resistance Protein (BCRP/ABCG2)的抑制
 
* *